The proposal is part of a long term project aimed at developing better analytical methods for determining the structures of important biomolecules such as peptides and oligosaccharides. Rapid advances in molecular biology and biochemistry are having a major impact on biomedical research, but depend heavily on structural analysis and in the last decade, mass spectrometry has emerged as one of the most sensitive and versatile tools in this endeavor. The PI has been involved in the mass spectrometric study of reactions for nearly 15 years, but since 1996 has turned his attention towards the biomedical applications of mass spectrometry. In the present proposal, the work focuses on developing gas phase reactions that can be used to probe structural features that have proven to be difficult to discern by conventional methods. Specifically, the focus will be on phosphopeptides and sialic acid containing oligosaccharides. These species play critical roles in biological systems, but are challenging to study by mass spectrometry because they readily lose key structural elements during the analysis (i.e., phosphate and sialic acid, respectively). Building from promising preliminary results involving gas phase reactions of phosphopeptides with boron-containing reagents, a set of studies has been designed to improve the efficacy of this methodology, test its generality, and probe its limitations. The methodology will then be extended to the analysis of sialic acid-containing oligosaccharides. Again, the boron reagent will be used to foster the retention of the key structural element, sialic acid, so that the nature of its linkage can be probed. As in the phosphopeptides, the work will focus on finding the best reaction conditions and will build from the analysis of simple to complex analytes. Finally, a small project will probe the reactions of gas phase salt complexes with an emphasis on chiral recognition. All of the experimental work will be supported by modern computational modeling including quantum mechanical and force-field calculations. The great majority of the studies will be completed in our mass spectrometry facility at San Francisco State University by undergraduate and graduate (masters) students as well as a post-doctoral fellow. A few studies requiring specialized equipment will be completed in collaboration with Dr. Richard O'Hair at the University of Melbourne.